I've been experimenting with CLS for the past few days, and trying to figure out how it works. From what I've read, the pop up flash from the camera fires a pre-flash which sends an IR signal to the flash giving it the appropriate information, such as the exposure or power output, and then triggers it. What I'm wondering is if the pop-up flash is supposed to have an effect on the final image. Whenever I fire the flash, you can obviously see the harsh reflections on the subject from the pop-up flash, which sort of defeats the purpose of bouncing the off camera flash off of an umbrella or through a softbox for a lighting that's less harsh.

Does anybody know of any ways to get around this? If I use a shutter speed higher than the sync speed, would the pop-up flash not appear in the final image? I know that Nikon sells a small plastic cover to prevent light from the pop-up flash from having any effect on the subject (for example, preventing them from blinking), but is it designed to prevent the flash from reflecting off of the subject during the exposure? Is the pop-up flash supposed to even be visible during the exposure? Even when I turn the pop-up to off (which I'm assuming is the "--" in the CLS menu on the camera) I still see quite a visible effect from the flash.

How can you set the pop up to not fire? The best that I've been able to get so far is getting minimal, but still visible, light from the pop up during the exposure. I went into the "custom setting menu", and under "bracketing/flash" I selected "Flash control for built in flash", followed by "commander mode" and I set the built in for "--", but I still get some flash power during the exposure. For instance, I was taking some portraits in the dark a few days ago, using my off camera speedlight as my sole source of lighting. However, because the pop-up fired I got some harsh lighting from the front, and got rid of the dark shadows that I was originally going for.

Does anybody have any solutions that will make sure that the pop up isn't visible at all? If needed, I could purchase the SG-3IR panel, but before I buy it I'd like to make sure that there's no solution that can be accomplished through the camera's menu.

I ended up doing just that, blocking the flash. By holding my hand a few centimeters away from the flash, it was still able to communicate with the slave unit, but it was cumbersome to have to hold my hand there throughout the entire shoot.

Would using the SG-3IR panel to block the visible light really be my only option? (Unless I built my own homemade version for the time being)

That's an idea, but would that block off the IR light that triggers the speedlight? Also, although the diffuser would cut down on the light and diffuse it, it still wouldn't completely eliminate it if I were going for that effect. For now I'll try putting some paper over the flash, I just hope that it doesn't overheat and melt, I couldn't see a pop-up flash being powerful enough to melt though.

On your menus, in Commander Mode, have you selected "--" for the on board flash and then clicked OK? If you've selected "--", but not OK, your on board flash will revert to TTL and still contribute to the final shot.

There is a specifically designed add-on to block all but the infrared light from the pop-up. I use it all the time when shooting test-charts to avoid reflections. You can see one here.
It effectively converts your pop-up into a remote IR commander - well almost: there is some light reflected back (behind the camera) from this gadget.

Thanks, Thomas. I got hold of a Nikon representative today using their live chat support, and they recommended using the SG-3IR as well (obviously a Nikon representative would recommend their own product, but it still seems like a good investment).